Out of Darkness
by The Clever Weasel
Summary: This is an alternate ending to Star Trek: Into Darkness, however, it takes a different turn as to what happens to Khan and the other Augments. And what's this about Khan having a wife and kid? Warning: there will be kissing! I own only the one OC!


It was two months after he had crashed the _Vengeance_ into downtown San Francisco, but Khan found himself still unfrozen and uncharged in a Star Fleet holding cell. The last thing he remembered before waking up in the cell was getting chased down by an emotionally constipated Vulcan on Miralax before the irritating linguist had shouted something about saving their blasted captain and the Vulcan had knocked him unconscious. He wasn't sure how long he'd been out, but he'd been in the cell for two months and five days. He only knew the number of days only because he got three meals per day and the lights were turned down for an eight hour period in between two of them and he had been keeping careful track.

But in that time, he had not seen one interviewer, lawyer, or even a 'Fleet officer. The only other life forms he saw were the people who brought him his food and took away the empty dishes. He had been provided with reading materials, all printed so that he couldn't hack anything, but it was still mind-numbingly boring in a twenty by twenty metal box with a bed, a sink, and a toilet.

But finally, after two months, there was a change. A Star Fleet admiral, whose name Khan didn't care about, and a security team came down to his cramped, boring patch of hell, handcuffed him, took him out of his cell, and loaded him into a transport. The admiral sat on one side of the transport while Khan was securely strapped into the other. The security team stood in formation between Khan and the admiral and the transport began moving.

"Where are we going?" Khan asked.

If looks could kill, Khan would be a smoldering pile of ash from the look the admiral gave him. The Augment merely searched the admiral's face and saw that he was seething about something pertaining to Khan and where they were headed.

"We are on our way to your hearing and then you will be off to your near home," growled the admiral.

"And where am I being relocated to?"

The admiral simply kept glaring at Khan and while the former dictator wanted to continue to badger until he was given answers, he settled for staring the admiral down in silence. The trip was short and Khan was taken from the transport, still handcuffed, and led into one of the buildings still standing at Star Fleet HQ and hustled down hall before being shoved into a room and before a panel of sever looking people who the admiral joined.

_'__Joy,'_ Khan though with a mental eye roll, '_more incompetent leadership.'_

"Khan Noonien Singh," the admiral in the middle addressed him, a man named Barnett if the name plate was anything to go by. "We feel the need to inform you that John Harrison was charged with treason and fifty-eight counts of murder before being executed at a maximum security penitentiary." As much as he hated to admit it, this caught him off guard. If John Harrison was dead, then what was to become of him? "We recently discovered that there is an Augment acculturation, rehabilitation, housing center here on Earth. You, Mr. Singh, are hereby ordered to go to this facility and attempt to lead a normal life. However, a hint of you attempting to plot world domination or overthrow any government, no matter how small and inconsequential, will result in your immediate incarceration until we dig your file up again in a few decades. You are being housed by the owner of this operation and will remain under their direct supervision. Dismissed."

_'__What the bloody hell just happened?'_ Khan wondered as he was led from the room and back to the transport. This time there were just two security officers, one of which he recognized as the chief of security on the _Enterprise_ and the irritable CMO of the same ship. Khan sat down across from the doctor with an unreadable expression, but on the inside he was still trying to figure out just what happened. As far as he could tell, they used a fake persona to take the fall and had let him off to go to some rehabilitation facility. Then it hit him. There was no conceivable way that they were truly sending him to a rehab facility. Far more than likely he was being sent to another lab for more tests and to be sucked dry of every idea he has ever had.

"Mr. Singh," the doctor all but growled as he looked up from the PADD he had been looking over. "I need to conduct a quick physical for your admittance to this facility. Shouldn't take but a moment." The doctor took out a tricorder and slowly scanned Khan. "Well look at that," said the doctor with a mock tone of fascination, "you're in better-than-perfect health."

"Where are we truly going doctor?" Khan asked in a bored tone.

"Your new home," said the doctor, "at the place where any and all augmented humans can call home and lead normal lives, without much scrutiny of Star Fleet or the public at large, as they adjust to life in this new time."

"There is no need to lie to be doctor," Khan said. "What is it that Star Fleet wants of me now?"

"They want you off their hands," said the doctor, his words blunt. "The place they are sending you is privately owned, operated, and funded. Granted, it did only crop up a little over a year ago."

A little over a year was how long he and his crew had been in Marcus' procession. Even if it wasn't Star Fleet holding his family over him, someone else was. The ride went on in silence for a bit more than two hours before they landed and an Asian man and a kid with curly hair, both in command gold, came out of the cockpit.

"We have arrived," said the Asian man with a grin on his face. Of course Khan recognized the pilot and navigator of the Enterprise, but he wanted to know why four members of the _Enterprise_ crew had been assigned to take him to his new home. Unless they were purposely sent and had called dibs on being able to torture him before the scientists got their hands on him to observe his healing abilities.

The curly headed kid opened the door and proceeded to more or less leap from the transport and go running off somewhere out of sight. The pilot gave a nod to the doctor and head of security before following his young friend. Khan was gently pulled to his feet by the head of security, much to his surprise, before he was led out of the transport. As near as he could tell he was somewhere in the Himalayas, if the massive snowcapped mountains and surrounding forests were any hint. But he stopped short with a small, energetic blur ran smack into chest and pulled him into a breathtaking hug. Literally, he could not breathe.

"Khan!" the woman shrieked before pulling back for a moment only to then draw him into another hug. This time Khan's lack of breath had nothing to do with the tight hug. When the woman had pulled back Khan had gotten good look at her soft face, her small nose, her curly bronze hair, and her sharp green eyes to know who she was.

"Kati?" he said looking down at her. The woman, Kati, took a step back from him and the _Enterprise_'s chief of security removed his cuffs.

"Duh," Kati said with a flippant tone and a massive grin. "Oh Khan," she said pulling him into yet another hug, this one he was able to return just as fiercely, "you're finally here. Thank you for bringing him here," she said to the Star Fleet officers, though she still didn't let go of her brother.

"It was our pleasure," the doctor said with a small grin. "Lucky us he didn't try to strangle us on sight,"

Kati laughed and the chief of security grinned widely. "No kidding," said Kati. "But I think I speak for all of us when I say that we are overjoyed that he is here," she said, her voice somber and she released Khan to nod at the officers.

"Who is 'we'?" Khan asked with some trepidation. 'We' could mean anything from Kati and one of his crewman, to Kati and all seventy-one other crew members.

"Everybody!" Kati said loudly throwing her hands up in the air. Khan gave a small smile when he remembered that Kati tended to be a talkative bundle of energy that would switch languages whenever she felt like it.

Khan hugged the woman he thought of as a little sister close to his chest and only barely kept from crying into her hair. "I thought I had lost you," he said.

"Yeah," came a male voice from Khan's left, "lucky for you were like cockroaches. We are near impossible to kill and always come back when adequate given time." Khan turned, still keeping a hold of Kati, and saw a tall, skinny brunet smirking at him with his arms crossed over his chest.

"Rodriquez?" Khan asked.

"Who else?" Rodriquez asked spreading his arms. But he smiled before taking Khan's hand in a handshake and pulling him into a hug with Kati laughing brightly beside them. "It's good to see you."

"You truly have no idea how happy I am to have you back," Khan said quietly.

"Actually," came an obnoxious voice Khan couldn't have been happier to hear. Sure enough, when he looked up, there as a blonde man with calculating brown eyes appraising him, "we are all caught up to date on everything that happened in the last three hundred years and, more specifically, the past year."

"McPherson," Khans said with fondness. He and the pilot were a lot like brothers and, while they picked on each other they did it out of love and grudging affection.

"Khan," the two shared a firm handshake and large smiles that felt just as intimate as a hug.

"It is 'bout time you get here," came a booming voice. Khan turned just in time to be facing the large, brown-haired Russian before he was grabbed in a bear hug.

"Otto," Khans said wrapping his arms as far around as they'd go on the massive scientist. "It is wonderful to see you again."

"Likewise," said Otto letting go of his brother.

"I want to hug Khan again!" was the only warning the past-emperor got before he was all but tackled by Kati and only just managed to stay on his feet.

"Kati," came a voice Khan would have sworn he'd never hear again, "let go of Khan before you crack his ribs and I have to set them."

After Kati released her death grip Khan turned slowly to where a slight Asian woman stood beside the _Enterprise_'s lead doctor. When Khan had been awakened he knew that twenty-seven cryotubes were lost. One of them contained the _Botany Bay_'s lead doctor, Ling. Ling who was now standing before him smiling.

"You look like you've seen a ghost," she said before gently hugging him. Khan felt hot tears slip down his cheeks as he tightly held the doctor and buried his face in her hair, his sister he had thought utterly beyond his reach.

"I feel like I am currently seeing one," he said quietly.

Ling gently pulled back. "Khan," she said softly, "when Kati said that everyone was here, she meant that everyone who was frozen on the _Botany Bay_ is here. You were the only one missing until now." Ling brushed a tear from her cheek while she smiled at her brother.

"But Marcus told me that he had seventy three cryotubes, including mine, and that the tubes had failed or he'd killed them with his bloody experiments. When… how…?" Khan didn't even know how such a thing could be possible.

The doctor, McCoy, stepped forward at this point. "That bastard son of a bitch Marcus only told you that the tubes had been disabled or failed to better control you. He knew that if you thought he would kill one of your crew if you stepped out of line, then he would tell you exactly that. But he only knew that one hundred tubes were on the ship because that's what was on the manifest. Unfortunately only twenty-seven tubes were transported to the _Enterprise_ before Marcus' people found them and counted them. When he did that we couldn't take anymore without showing him that the other twenty seven were still around, just not in his hands. He would have come looking for them before we were ready for him to."

"I don't understand," said Khan. And he truly was at a total loss. Why would the _Enterprise_ steal twenty seven of his family from Marcus even before… everything. How did they even know about the ship at all? He was missing a key piece of information that would make everything else fall into place, but he hadn't the slightest idea what it could be.

"Khan," McPherson said slowly. "Do you remember Nala?"

Khan stared McPherson down. How could he not remember Nala? His _wife_? The woman who he'd had to leave behind? When Khan had seen the end of the war coming, and the odds not lying in his favor, he'd hidden his wife away before he was exiled. The memory of her hurt far more than he'd ever share, but, despite his best efforts and almost a month of sleepless nights, he had never found out what had happened to her and given up. While he was with Marcus he searched for her, but could never find her, granted she was a clever and highly intelligent woman; she was an Augment after all.

"How could I forget?" Khan asked softly, through his voice nearly cracked.

"Khan," Ling said gently, "she survived. She's still alive today. She is the reason this haven exists for us."

"Nala is alive?" Khan asked, his voice scarcely above a whisper. His mind was suddenly elsewhere and his eyes are scouring the surrounding looking for her straight blonde hair and pale blue eyes.

"Khan," McPherson said. "There's more and you need to see this." McPherson began walking over a rise that separated them from the rest of the valley and Khan followed him. Once they got to the top of the rise the whole valley was spread out before them. There were several houses arranged in rows. A few farms could be seen raising corn and wheat. There was even what looked like an observatory connected to a science lab, both of which were across from a medical building that appeared to be both operating and teaching.

"We call it home," said Ling. "It's got a bit of everything and we can study all sorts of things here and get caught up on all the advancements made in three hundred years."

"What part does Nala play in all this?" Khan asked. "Did she create this place?"

"Kinda sorta," said McPherson. "Both her… and your son."

Khan felt the world stop beneath his feet. His brain seemed shut down on him and was sure taking its sweet time with rebooting. His… son? His Nala had been pregnant when he hid her away? Had he left his wife _alone_ while she was pregnant?!

"Khan!" Kati shouted in his ear at the same time as Otto slapped him on the back.

"I have a son?" Khan asked after getting viciously yanked from his zone out.

"Yup," said Rodriquez.

"How…?"

"We aren't for sure," said Rodriquez.

"Nala can tell you the whole story," said McPherson. "We've only heard small bits and pieces."

"Where is Nala?" Khan asked.

"She should be coming out of the library any minute now," said Ling.

Khan quickly located the library among the other buildings between one of the local shops and the houses. He kept his eyes on the doors until they opened. He wanted to strangle someone when the curly Russian kid came out laughing, until he saw Nala walk out through the door the young Star Fleet officer held open for her. Khan stared.

_'__It has been three hundred years,'_ he had to remind himself. Nala didn't look twenty anymore, she looked closer to fifty. Her blonde hair hung a little more limp and was beginning to grey. She walked a little slower, but her mind still appeared above and beyond if her sharp eyes were anything to go by, even if they did have a few wrinkles around them. But in his eyes, she was just as beautiful as they day they finally got together.

Khan walked slowly down the slope until he was halfway down and Nala's eyes seemed drawn to him. Both of them stopped walking and Nala's easy going smile slipped off her face. She said good-bye to the Russian kid before she began walking towards Khan. Her gaze went from sharp to cutting. Khan stayed stock still as she approached. He couldn't help it. Nala had always seemed to have this power over him. He could never refuse her, but she was always an open book to him. But now he couldn't get a read on her, but she was eyeing him like a mother bear.

Soon they were standing just less than two feet apart. Khan could easily reach out and touch her, but the way she was staring at him was seriously putting him on edge. Nala suddenly socked him across the jaw and Khan was sent sprawling into the grass. He touched his jaw before looking up at her. She was glaring at him. At least until she grabbed him by the collar of his shirt and dragged him into a bruising kiss. Khan got his feet underneath himself and returned the kiss with just as much passion. The kiss seemed too short, but at the same time it seemed to last forever. But eventually the pair separated and Khan stared into Nala's eyes.

"I missed you so much," Khan said. "Ever since I awoke… I looked for you," he said and rested his forehead against hers.

"I know, I knew you would," she said softly as she closed her eyes. "I missed you too and I knew you would look for me. But as soon as I found out the _Botany Bay_ had been found I got to work on this place," she said gesturing to the small town. "Everything was almost together, but just needed a few more things to get it up and running. It's a shame we couldn't get our hands on all one hundred cryotubes right away," Nala said sadly.

"How did you manage to get ahold of twenty-seven to begin with?" Khan asked.

"I have a man on the _Enterprise_ who keeps me informed and can pull strings without raising flags," Nala said with a sly smile up at Khan.

"Underneath that fool Kirk I'm not surprised," Khan snarled.

"What's wrong with the captain?" Nala asked. "Our boy thinks he's a fine man."

"Kirk is nothing more than an egotistical child who relies on luck far more often than he should. Our son should be the captain but instead gets orders from some lowly human."

"Mm-hm," said Nala.

"Speaking of which," Khan said slowly. "I am so sorry for leaving you alone while you were pregnant. I didn't know-"

"Khan," said Nala with a soft smile, "I didn't even know I was pregnant until two months after you had been banished. Our last night together was his date of conception. You had no way of knowing. Plus, it turned out alright in the end."

"I still should not have left you," Khan said hugging her tighter.

"Everything worked out," Nala said. "Speaking of everything working out, what happened to Captain Kirk?"

"I do not know," Khan said. "But whatever it was they needed my blood to help him."

"Leonard," Nala said, her voice much like a mother who wouldn't be lied to. "What happened to the captain?"

"He died in the warp core chamber," Doctor McCoy said slowly and took a couple of steps back.

Nala seemed to become totally stiff in Khan's arms.

"He. Did. What?" Nala snarled and pushed Khan away from herself and began stalking back towards town.

"Nala…" Khan began.

But Nala was too drawn up in her own thoughts. She hadn't been told why the captain couldn't discuss Khan's release into her custody with the Admiralty because of health and political reasons. But the brat had up and died in a warp core. Her mind was racing with the side effects of irradiated cells and the consequences thereof. She stormed into the observatory causing other Augments that Khan recognized to scramble out of her way.

"James!" she roared when she caught sight of the blonde captain.

"What?" he all but squeaked.

"You died?!" she thundered. "You died in a warp core and all you tell me is that you were recovering from injuries received when the ship fell through the atmosphere and then got caught up in the bureaucratic bullshit?! You died and you lied to me about it?!"

"I didn't want you to worry," said the captains slowly drawing closer, but kept his hands up in surrender.

"Worry?" she growled.

"Okay fine," he said dropping his hands and rolling his eyes. "Whenever I get hurt you turn into helicopter mom and are always hovering. As it was, I was unconscious, then loopy on drugs for the first couple days and then sore as all hell. _And then_ I was dragged into the bureaucratic bullshit. I didn't need you nagging me too."

"Helicopter mom?" she asked. She still didn't sound happy, but her eyes were soft.

"Yes, Mama," Jim said and pulled his mother into a hug. "But see, I'm fine now. Bones did a great job patching me up."

Khan brain however seemed to have short circuited before it rolled over and died. _Mama_? Nala's son, _his son_, was Kirk? He had threatened his own son and his son's new extended family. But then again Kirk had threatened him with their family. Maybe he hadn't known. After all how could he know that his extended family was inside the torpedoes until Khan told him to open one? But _Jim Kirk_ was his son? Then again, who else would be able to be in the right spot to steal twenty-seven cryotubes and done so without raising any flags to anyone other than an Augment. So all he knew was that he was chasing a rogue Augment when he hunted Khan to Qo'noS? Unless Kirk knew that Khan was his father. Did he know? Khan realized that he was in desperate need of answers and was coming up severely lacking. But Kirk, his son, had died in the_ Enterprise's_ warp core when the ship was plummeting to Earth after he had shot it down? He had given his life to save his crew. Khan felt a tear slip out of the corner of his eye as all of the recent events and their true unfolding caught up to him. Kirk knew most of what was going on the entire time, but had played Khan in order to incriminate Marcus and save his crew. But also died in the process. That's why the Vulcan had been so hell bent on getting his blood.

"Um," came Kirk's voice drawing Khan out of his thoughts. "Are you alright?"

"Fine," Khan just managed to get out.

"Really?" Kirk wasn't at all convinced. "Because you look like hell." Oh he was definitely his mother's son. He had her blonde hair, but his eyes were a brighter blue and his time spent in the sun had given him more of a tan, but he had Khan's complexion. And now that Khan was looking he could see it. Sure, Kirk, _James_, looked more like Nala, but he still had Khan in the way he held himself and even his smile, not that James had ever seen Khan smile. But he had Nala's tendency for trouble and her disregard for a chain of command.

Nala scoffed. "Khan just got some surprise information is all," she said with her trouble-maker grin that she had kept all those years.

"What?" James asked. "That his whole crew is still alive?"

"James," Nala said slowly. "Meet your father," she said looking at Khan.

_'__So she hadn't told him,'_ Khan realized.

"What?" James asked after a minute of staring at Khan.

"Yup," Nala said.

James stared at him and Khan would have fidgeted under the intense gaze if he were a lesser human. But where had this cold stare been on the _Enterprise_? Where had his strength been on Qo'noS? What about his savagery on the _Vengeance_? Kirk didn't act anything like an augment. He was brash and arrogant and seemed to only have half a plan half of the time.

"Interesting," James muttered quietly, but Khan could still hear it. The other Augments in the room looked between the two like they were two tigers being introduced for the first time. But they probably weren't far off.

"I didn't know-," Khan said before breaking off.

"No I figured," Jim said cutting him off. "I only knew that you were some terrorist until we got to Qo'noS and I tried punching you in the face. It's a lot like punching Ling in the face, except Ling actually punches me back. But that was only my first clue and I hadn't put two and two together yet. When you said your name was Khan that's when I figured it out. But Mama here never told me who my dad was, just that he was important or something like that."

"Yeah," Nala scoffed and gave Jim a playful glare. "Something like that."

"It's nice to see you under better, more friendly, circumstances though," said Jim. "I was a little afraid that the 'Fleet was going to sink their teeth into you until Spock suggested executing John Harrison and putting Khan Singh here."

"I thought the same," said Khan taking a step closer to his son. It was a strange thought, but it felt nice all the same. "If you are indeed a full blooded Augment, then why didn't you hit me harder on Qo'noS?" asked Khan.

"My best friend, and doctor, Leonard McCoy, or as I call him Bones," the doctor huffed and muttered something about infants under his breath, "worked with Mama here to make a serum that nullifies the physical effects of Augmentation. It allowed me to still think and have the augmented senses, but I still had to try in physical fitness classes. Over all, it made it easier to hide in plain sight."

"Yeah," said Ling coming up behind Jim and putting him in a headlock, "the kid here likes to show off," she said ruffling his hair. Jim got out of the headlock with a smile on his face and his hair all askew and managed to ruffle Ling's hair.

"I'm only a few decades younger than you," said Jim. "And if we're taking time in cryosleep out of the equation, then technically Mama is the only one older than me."

"Did you just call me old?" Nala asked.

James seemed to freeze. "Maybe?" he said, though it was more of a question. Nala cocked an eyebrow. "Okay, I may have implied that you are old in years, but those years have made you far more wise than all of us."

"Ass kisser," McCoy muttered.

"Shut up," James whispered out of the side of his mouth before giving Nala a thousand watt grin. Nala only chuckled at the two men before wrapping her hands around Khan's arm and holding onto it. "So can I show...Dad– wow that's weirder to say than I ever thought it would be– around the place?"

"Only if you don't mind me tagging along," said Nala with a teasing smirk. "And don't think I've forgotten about you dying and not telling me about it," said Nala in a seriousness. "You know I find out everything eventually."

"Not everything," said James with a thoughtful expression. Nala gave him the look that said: 'I am your mother, therefore I know you and all of your deepest, darkest secrets.' "I mean pretty close, but not quite."

"What don't I know then?" asked Nala.

"What I got you for your birthday," James said with a big grin.

"My birthday?" asked Nala.

Khan froze and Nala stopped with him. Jim stopped a few steps later and turned back to his parents looking confused.

"Today is your birthday," Khan said looking at her. "Happy birthday." She gave him a soft smile and Khan put his hand on her cheek before their lips met in a long deep kiss. They kissed for a good long while and when they parted they put their heads together just enjoying being in each other's presence.

"This is really weird," said James. Khan and Nala turned to where Jim was sitting cross legged on the ground with his elbows on his knees and balancing his head on his fists. "I've never seen Mama kiss anybody like that before. I mean I've seen her kiss people to distract them before breaking their neck or shooting them in the face, but I've never seen her kiss someone she is in love with."

"James," said Nala smiling fondly at him. "Grow up and don't ruin my moment." Khan found himself smiling softly at his little family he didn't know he had but he knew he was going to love. "And what did you get me for my birthday?"

"Not telling!" he crowed before he jumped up and dusted off his pants. "So over there are the labs, we've got everything for whatever you want to study and if we don't have it, let me know and I'll go find one. The library had all kinds of history, journals, and documentaries if you want to actually catch up on the finer details of the last three hundred years. Or you can just ask Mama. After all, Mama knows all. Over there–"

Khan let his son's voice become background noise as he looked around at his new home. He may no longer have a quarter of the planet under his domain, but he had everything he could ever hope for a more. And with Nala by his side and James gallivanting off into trouble, he knew he'd never be in want for anything for a long time to come.

* * *

**So that is my first ever one shot. I hope you all enjoyed. If you have any suggestions or you notice and discrepancies or a plain old mistake please let me know. I do actually read comments.**

**My other fics are currently on a sort of hiatus while I figure out exactly what is going to happen and where I am taking them. That and really random plot bunnies keep showing up out of absolutely no where and distracting me.**

**As always, comments give authors the warm fuzzies. Thanks for reading!**


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